Testing of Multifractional Brownian Motion

Total Page:16

File Type:pdf, Size:1020Kb

Testing of Multifractional Brownian Motion entropy Article Testing of Multifractional Brownian Motion Michał Balcerek *,† and Krzysztof Burnecki † Faculty of Pure and Applied Mathematics, Hugo Steinhaus Center, Wroclaw University of Science and Technology, Wyspianskiego 27, 50-370 Wroclaw, Poland; [email protected] * Correspondence: [email protected] † These authors contributed equally to this work. Received: 18 November 2020; Accepted: 10 December 2020; Published: 12 December 2020 Abstract: Fractional Brownian motion (FBM) is a generalization of the classical Brownian motion. Most of its statistical properties are characterized by the self-similarity (Hurst) index 0 < H < 1. In nature one often observes changes in the dynamics of a system over time. For example, this is true in single-particle tracking experiments where a transient behavior is revealed. The stationarity of increments of FBM restricts substantially its applicability to model such phenomena. Several generalizations of FBM have been proposed in the literature. One of these is called multifractional Brownian motion (MFBM) where the Hurst index becomes a function of time. In this paper, we introduce a rigorous statistical test on MFBM based on its covariance function. We consider three examples of the functions of the Hurst parameter: linear, logistic, and periodic. We study the power of the test for alternatives being MFBMs with different linear, logistic, and periodic Hurst exponent functions by utilizing Monte Carlo simulations. We also analyze mean-squared displacement (MSD) for the three cases of MFBM by comparing the ensemble average MSD and ensemble average time average MSD, which is related to the notion of ergodicity breaking. We believe that the presented results will be helpful in the analysis of various anomalous diffusion phenomena. Keywords: multifractional Brownian motion; autocovariance function; power of the statistical test; Monte Carlo simulations 1. Introduction Over the last decades, massive advances in single-particle tracking (SPT), partially based on superresolution microscopy of fluorescently tagged tracers, or fluorescence correlation spectroscopy allow experimentalists to obtain insight into the motion of submicron tracer particles or even single molecules in complex environments, such as living biological cells, down to nanometer precision and at submillisecond time resolution [1,2]. The observed data obtained by SPT experiments often show pronounced deviations from Brownian motion, namely, anomalous diffusion of the power-law form 2 a EX(t) ' Kat (1) of the mean-squared displacement (MSD) is observed [3–8]. Ka is the anomalous diffusion coefficient. Depending on the magnitude of the anomalous diffusion exponent a we distinguish subdiffusion for 0 < a < 1 from superdiffusion with a > 1 [5,8]. Subdiffusion is typically observed for submicron particles in both bacterial and eukaryotic cells [6,9–13], in artificially crowded [14,15] and structured [16–19] liquids, in pure and protein-crowded lipid bilayer systems [12,20–25], as well as in groundwater systems [26]. Superdiffusion occurs in the presence of active motion, for instance, in living biological cells [27–29] or due to bulk-surface exchange [30,31]. While typically anomalous Entropy 2020, 22, 1403; doi:10.3390/e22121403 www.mdpi.com/journal/entropy Entropy 2020, 22, 1403 2 of 17 diffusion refers to the power-law behavior (1) with a fixed a, an increasing number of systems are reported in which the local scaling exponent of the MSD (1) is an explicit function of time, a(t). Such transient behavior has, for instance, been observed for green fluorescent proteins in cells or for the motion of lipid molecules in protein-crowded bilayer membranes [25,32]. Fractional Brownian motion (FBM) introduced by Kolmogorov in 1940 and rediscovered by Mandelbrot and van Ness in 1968 [33–35] is a generalization of the classical Brownian motion (BM). Most of its statistical properties are characterized by the self-similarity (Hurst) index 0 < H < 1. FBM is D H H-self-similar, namely for every c > 0 we have BH(ct) = c BH(t) in the sense of all finite dimensional distributions, and has stationary increments. It is the only Gaussian process satisfying these properties. FBM is the overdamped description for viscoelastic motion and thus intimately connected to the fractional Langevin processes, an attractive framework for many physical systems [36], for instance, 2 2 2H of lipid molecules in bilayer membranes [22,25,37]. The second moment of FBM reads EBH(t) = s t , 2 2 where EBH(1) = s > 0. As a consequence, for H < 1/2 we obtain subdiffusive dynamics with persistent motion, whereas for H > 1/2, the process is superdiffusive and antipersistent. Since FBM is the classical model for power-law dependence a number of statistical tests have been already introduced for this process in the literature. Let us mention here the tests based on the autocovariance function (ACVF), MSD, and detrending moving average statistics [38–40]. FBM has stationary increments that do not allow us to model processes whose regularity of paths and “memory depth” change in time [41]. Several generalizations of FBM have been proposed recently. One of these, called multifractional Brownian motion (MFBM), was proposed by Peltier and Véhel [42] with time-varying Hurst exponent H(t) which is a Hölder function. The variance at time 2 2H(t) t of the MFBM BH(t)(t) is given by Var(BH(t)(t)) = s t [43]. The time-varying Hurst exponent H(t) characterizes the path regularity of the process at time t: sample paths near t with small Ht, close to 0, are space-filling and highly irregular, while paths with large Ht, close to 1, are very smooth. The variance constant s2 determines the “energy level” of the process. This natural extension of FBM results in some loss of some of FBMs basic properties, in particular, the increments of MFBM are non-stationary and the process is no longer self-similar. Other, similar generalizations are limited to a piecewise constant H [44] but, what is important from a data analysis point of view, is that they lead to continuous Gaussian processes with stationary increments. Let us also mention an idea involving an appropriate class of covariance functions. Ryvkina [45] uses such covariance functions to define Gaussian processes to extend FBM and MFBM to a class of fractional Brownian motions with a variable Hurst parameter parameterized by a set of all measurable functions with values in (1/2, 1), and different from MFBMs. However, from a biological data point of view, such a range for H values is not practical since it only corresponds to a superdiffusive (long-range dependent) case. MFBMs have become popular as flexible models in describing real-life signals of high-frequency features in geoscience, microeconomics, and turbulence, to name a few [43]. They are closely related to the notion of transient diffusion dynamics observed in biological experiments. The article is structured as follows. In Section2, the MFBM is defined and its basic properties are presented. We also recall formulas for the ensemble average MSD, time average MSD, and present three Hurst exponent functions that will be analyzed in the sequel. In Section3, the main results are presented. We introduce a statistical test on MFBM based on its ACVF which is presented as a quadratic form. Next, the power of the test is studied for the three cases corresponding to different Hurst exponent functions. We show the areas where the test is very strong in distinguishing between the processes and the cases when it fails in this respect. Finally, Section4 summarizes and concludes our work. 2. Model and Methods Let us start with a definition of the MFBM. Entropy 2020, 22, 1403 3 of 17 Definition 1. (Multifractional Brownian motion). Process BH(t)(t) is called a multifractional Brownian t≥0 motion (MFBM) if it is a centered Gaussian process with covariance function H(t)+H(s) H(t)+H(s) H(t)+H(s) Cov(BH(t)(t), BH(s)(s)) = D(H(t), H(s)) t + s − jt − sj , (2) where p s2 G(2x + 1)G(2y + 1) sin(px) sin(py) D(x, y) = (3) x+y 2G(x + y + 1) sin p 2 for some s > 0 and Hölder function H : [0, ¥) ! [a, b] ⊂ (0, 1) of some exponent b > 0 [46]. 2 ( ) = 2 2H(t) ( ) The second moment of MFBM scales as E BH(t) t s t . Hence, we will call H t the Hurst exponent function. Furthermore, for H(t) ≡ H 2 (0, 1) MFBM becomes standard FBM. de f In general, MFBM has non-stationary increments. Its increment process Y(t) = BH(t+1)(t + 1) − BH(t)(t) possesses the long-range dependence property, in the sense that ¥ 8d > 0, 8s ≥ 0 ∑ jCorr (Y(s), Y(s + kd)) j = +¥, k=0 ( ( ) ( )) where Corr is the correlation function, i.e., Corr(Y(t), Y(s)) = pCov Y t ,Y s [46]. E2Y(t)E2Y(s) Furthermore, the function H(t) can be pointwise interpreted as a local self-similarity parameter, i.e., ! BH(u+#t)(u + #t) − BH(u)(u) lim = s(u) (BH(t))t2 , #!0+ #H(u) R+ t2R+ where BH is a fractional Brownian motion with index H ≡ H(u), s(u) is a scaling function [47] and the convergence is on the space of continuous functions endowed with the topology of the uniform convergence on compact sets. 2.1. Mean-Squared Displacement Let us now recall different estimators of the MSD for a sample of n trajectories X1, X2, ... Xn, each with N observations, that is, Xi consists of Xi(t1), Xi(t2), ... , Xi(tN) equally spaced in time, i = 1, 2, . , n. Ensemble average MSD (EAMSD) is defined as follows: n 1 2 EAMSD(t = mDt) = ∑ (Xk(t1 + t) − Xk(t1)) , (4) n k=1 where m = 1, .
Recommended publications
  • Impact of Bacteria Motility in the Encounter Rates with Bacteriophage in Mucus Kevin L
    www.nature.com/scientificreports OPEN Impact of bacteria motility in the encounter rates with bacteriophage in mucus Kevin L. Joiner1,2*, Arlette Baljon3,7, Jeremy Barr 4, Forest Rohwer5,7 & Antoni Luque 1,6,7* Bacteriophages—or phages—are viruses that infect bacteria and are present in large concentrations in the mucosa that cover the internal organs of animals. Immunoglobulin (Ig) domains on the phage surface interact with mucin molecules, and this has been attributed to an increase in the encounter rates of phage with bacteria in mucus. However, the physical mechanism behind this phenomenon remains unclear. A continuous time random walk (CTRW) model simulating the difusion due to mucin-T4 phage interactions was developed and calibrated to empirical data. A Langevin stochastic method for Escherichia coli (E. coli) run-and-tumble motility was combined with the phage CTRW model to describe phage-bacteria encounter rates in mucus for diferent mucus concentrations. Contrary to previous theoretical analyses, the emergent subdifusion of T4 in mucus did not enhance the encounter rate of T4 against bacteria. Instead, for static E. coli, the difusive T4 mutant lacking Ig domains outperformed the subdifusive T4 wild type. E. coli’s motility dominated the encounter rates with both phage types in mucus. It is proposed, that the local fuid-fow generated by E. coli’s motility combined with T4 interacting with mucins may be the mechanism for increasing the encounter rates between the T4 phage and E. coli bacteria. Phages—short for bacteriophages—are viruses that infect bacteria and are the most abundant replicative biolog- ical entities on the planet1,2, helping to regulate ecosystems and participating in the shunt of nutrients and the control of bacteria populations3.
    [Show full text]
  • Non-Gaussian Behavior of Reflected Fractional Brownian Motion
    Non-Gaussian behavior of reflected fractional Brownian motion Alexander H O Wada1,2, Alex Warhover1 and Thomas Vojta1 1 Department of Physics, Missouri University of Science and Technology, Rolla, MO 65409, USA 2 Instituto de F´ısica, Universidade de S˜aoPaulo, Rua do Mat˜ao,1371, 05508-090 S˜aoPaulo, S˜aoPaulo, Brazil January 2019 Abstract. A possible mechanism leading to anomalous diffusion is the presence of long-range correlations in time between the displacements of the particles. Fractional Brownian motion, a non-Markovian self-similar Gaussian process with stationary increments, is a prototypical model for this situation. Here, we extend the previous results found for unbiased reflected fractional Brownian motion [Phys. Rev. E 97, 020102(R) (2018)] to the biased case by means of Monte Carlo simulations and scaling arguments. We demonstrate that the interplay between the reflecting wall and the correlations leads to highly non-Gaussian probability densities of the particle position x close to the reflecting wall. Specifically, the probability density P (x) develops a power-law singularity P xκ with κ < 0 if the correlations are positive (persistent) and κ > 0 ∼ if the correlations are negative (antipersistent). We also analyze the behavior of the large-x tail of the stationary probability density reached for bias towards the wall, the average displacements of the walker, and the first-passage time, i.e., the time it takes for the walker reach position x for the first time. Keywords: Anomalous diffusion, fractional Brownian motion Contents arXiv:1811.06130v2 [cond-mat.stat-mech] 29 Mar 2019 1 Introduction 2 2 Normal diffusion 3 3 Fractional Brownian motion 5 4 Unbiased reflected fractional Brownian motion 6 CONTENTS 2 5 Biased reflected fractional Brownian motion 7 6 Monte Carlo simulations 10 6.1 Method ...................................
    [Show full text]
  • Arxiv:2011.02444V1 [Cond-Mat.Stat-Mech] 4 Nov 2020 Short in One Important Respect: It Does Not Consider a Jump Over Obstacles, We fix Their Radius As = 10 
    Scaling study of diffusion in dynamic crowded spaces H. Bendekgey,1, 2 G. Huber,1 and D. Yllanes1, 3, ∗ 1Chan Zuckerberg Biohub, San Francisco, California 94158, USA 2University of California, Irvine, California 92697, USA 3Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), 50009 Zaragoza, Spain (Dated: November 5, 2020) We study Brownian motion in a space with a high density of moving obstacles in 1, 2 and 3 dimensions. Our tracers diffuse anomalously over many decades in time, before reaching a diffusive steady state with an effective diffusion constant Deff that depends on the obstacle density and diffusivity. The scaling of Deff, above and below a critical regime at the percolation point for void space, is characterized by two critical exponents: the conductivity µ, also found in models with frozen obstacles, and , which quantifies the effect of obstacle diffusivity. Introduction. Brownian motion in disordered media times. Most works, however, have concentrated on the has long been the focus of much theoretical and experi- transient subdiffusive regime rather than on the diffusive mental work [1, 2]. A particularly important application steady state. has more recently emerged, thanks to the ever increas- Here we study Brownian motion in such a dynamic, ing quality of microscopy techniques: that of transport crowded space and characterize how the long-time dif- inside the cell (see, e.g., [3–6] for some pioneering stud- fusive regime depends on obstacle density and mobility. ies or [7–10] for more recent overviews). Indeed, it is Using extensive numerical simulations, we compute an ef- now possible to track the movement of single particles fective diffusion constant Deff for a wide range of obstacle inside living cells, of sizes ranging from small proteins concentrations and diffusivities in one, two and three spa- to viruses, RNA molecules or ribosomes.
    [Show full text]
  • Random Walk Calculations for Bacterial Migration in Porous Media
    800 Biophysical Journal Volume 68 March 1995 80Q-806 Random Walk Calculations for Bacterial Migration in Porous Media Kevin J. Duffy,* Peter T. Cummings,** and Roseanne M. Ford** ·Department of Chemical Engineering and *Biophysics Program, University of Virginia, Charlottesville, Virginia 22903-2442 USA ABSTRACT Bacterial migration is important in understanding many practical problems ranging from disease pathogenesis to the bioremediation of hazardous waste in the environment. Our laboratory has been successful in quantifying bacterial migration in fluid media through experiment and the use of population balance equations and cellular level simulations that incorporate parameters based on a fundamental description of the microscopic motion of bacteria. The present work is part of an effort to extend these results to bacterial migration in porous media. Random walk algorithms have been used successfully to date in nonbiological contexts to obtain the diffusion coefficient for disordered continuum problems. This approach has been used here to describe bacterial motility. We have generated model porous media using molecular dynamics simulations applied to a fluid with equal sized spheres. The porosity is varied by allowing different degrees of sphere overlap. A random walk algorithm is applied to simulate bacterial migration, and the Einstein relation is used to calculate the effective bacterial diffusion coefficient. The tortuosity as a function of particle size is calculated and compared with available experimental results of migration of Pseudomonas putida in sand columns. Tortuosity increases with decreasing obstacle diameter, which is in agreement with the experimental results. INTRODUCTION Modem production of synthetic organic compounds has re­ rotational direction of the flagellar motors of the bacteria.
    [Show full text]
  • Diffusion on Fractals and Space-Fractional Diffusion Equations
    Diffusion on fractals and space-fractional diffusion equations von der Fakult¨at f¨ur Naturwissenschaften der Technischen Unversit¨at Chemnitz genehmigte Disseration zur Erlangung des akademischen Grades doctor rerum naturalium (Dr. rer. nat.) vorgelegt von M.Sc. Janett Prehl geboren am 29. M¨arz 1983 in Zwickau eingereicht am 18. Mai 2010 Gutachter: Prof. Dr. Karl Heinz Hoffmann (TU Chemnitz) Prof. Dr. Christhopher Essex (University of Western Ontario) Tag der Verteidigung: 02. Juli 2010 URL: http://archiv.tu-chemnitz.de/pub/2010/0106 2 3 Bibliographische Beschreibung Prehl, Janett Diffusion on fractals and space-fractional diffusion equations Technische Universit¨at Chemnitz, Fakult¨at fur¨ Naturwissenschaften Dissertation (in englischer Sprache), 2010. 99 Seiten, 43 Abbildungen, 3 Tabellen, 71 Literaturzitate Referat Ziel dieser Arbeit ist die Untersuchung der Sub- und Superdiffusion in frak- talen Strukturen. Der Fokus liegt auf zwei separaten Ans¨atzen, die entspre- chend des Diffusionbereiches gew¨ahlt und variiert werden. Dadurch erh¨alt man ein tieferes Verst¨andnis und eine bessere Beschreibungsweise fur¨ beide Bereiche. Im ersten Teil betrachten wir subdiffusive Prozesse, die vor allem bei Trans- portvorg¨angen, z.B. in lebenden Geweben, eine grundlegende Rolle spielen. Hierbei modellieren wir den fraktalen Zustandsraum durch endliche Sierpin- ski Teppiche mit absorbierenden Randbedingungen und l¨osen dann die Mas- tergleichung zur Berechnung der Zeitentwicklung der Wahrscheinlichkeitsver- teilung. Zur Charakterisierung der Diffusion auf regelm¨aßigen und zuf¨alligen Teppichen bestimmen wir die Abfallzeit der Wahrscheinlichkeitsverteilung, die mittlere Austrittszeit und die Random Walk Dimension. Somit k¨onnen wir den Einfluss zuf¨alliger Strukturen auf die Diffusion aufzeigen. Superdiffusive Prozesse werden im zweiten Teil der Arbeit mit Hilfe der Dif- fusionsgleichung untersucht.
    [Show full text]
  • Probing Microscopic Origins of Confined Subdiffusion by First-Passage Observables
    Probing microscopic origins of confined subdiffusion by first-passage observables S. Condamin*, V. Tejedor*, R. Voituriez*, O. Be´nichou*†, and J. Klafter‡ *Laboratoire de Physique The´orique de la Matie`re Condense´e (Unite´Mixte de Recherche 7600), case courrier 121, Universite´Paris 6, 4 Place Jussieu, 75255 Paris Cedex, France; and ‡School of Chemistry, Tel Aviv University, Tel Aviv 69978, Israel Communicated by Robert J. Silbey, Massachusetts Institute of Technology, Cambridge, MA, December 22, 2007 (received for review November 14, 2007) Subdiffusive motion of tracer particles in complex crowded environ- a ments, such as biological cells, has been shown to be widespread. This deviation from Brownian motion is usually characterized by a sub- linear time dependence of the mean square displacement (MSD). However, subdiffusive behavior can stem from different microscopic scenarios that cannot be identified solely by the MSD data. In this article we present a theoretical framework that permits the analytical calculation of first-passage observables (mean first-passage times, splitting probabilities, and occupation times distributions) in disor- dered media in any dimensions. This analysis is applied to two representative microscopic models of subdiffusion: continuous-time random walks with heavy tailed waiting times and diffusion on fractals. Our results show that first-passage observables provide tools to unambiguously discriminate between the two possible microscopic b scenarios of subdiffusion. Moreover, we suggest experiments based on first-passage observables that could help in determining the origin of subdiffusion in complex media, such as living cells, and discuss the implications of anomalous transport to reaction kinetics in cells. anomalous diffusion ͉ cellular transport ͉ reaction kinetics ͉ random motion n the past few years, subdiffusion has been observed in an Iincreasing number of systems (1, 2), ranging from physics (3, 4) PHYSICS or geophysics (5) to biology (6, 7).
    [Show full text]
  • Anomalous Diffusion in the Dynamics of Complex Processes
    Anomalous diffusion in the dynamics of complex processes Serge F. Timashev,1,2 Yuriy S. Polyakov,3 Pavel I. Misurkin,4 and Sergey G. Lakeev1 1Karpov Institute of Physical Chemistry, Ul. Vorontsovo pole 10, Moscow 103064, Russia 2Institute of Laser and Information Technologies, Russian Academy of Sciences, Troitsk, Pionerskaya str. 2, Moscow Region, 142190, Russia 3USPolyResearch, Ashland, PA 17921, USA 4Semenov Institute of Physical Chemistry, Russian Academy of Sciences, Ul. Kosygina 4, Moscow 19991, Russia Anomalous diffusion, process in which the mean-squared displacement of system states is a non-linear function of time, is usually identified in real stochastic processes by comparing experimental and theoretical displacements at relatively small time intervals. This paper proposes an interpolation expression for the identification of anomalous diffusion in complex signals for the cases when the dynamics of the system under study reaches a steady state (large time intervals). This interpolation expression uses the chaotic difference moment (transient structural function) of the second order as an average characteristic of displacements. A general procedure for identifying anomalous diffusion and calculating its parameters in real stochastic signals, which includes the removal of the regular (low- frequency) components from the source signal and the fitting of the chaotic part of the experimental difference moment of the second order to the interpolation expression, is presented. The procedure was applied to the analysis of the dynamics of magnetoencephalograms, blinking fluorescence of quantum dots, and X-ray emission from accreting objects. For all three applications, the interpolation was able to adequately describe the chaotic part of the experimental difference moment, which implies that anomalous diffusion manifests itself in these natural signals.
    [Show full text]
  • Normal and Anomalous Diffusion: a Tutorial
    Normal and Anomalous Diffusion: A Tutorial Loukas Vlahos, Heinz Isliker Department of Physics, University of Thessaloniki, 54124 Thessaloniki, Greece Yannis Kominis, and Kyriakos Hizanidis School of Electrical and Computer Engineering, National Technical University of Athens, 15773 Zografou, Athens, Greece Abstract The purpose of this tutorial is to introduce the main concepts behind normal and anomalous diffusion. Starting from simple, but well known experiments, a series of mathematical modeling tools are introduced, and the relation between them is made clear. First, we show how Brownian motion can be understood in terms of a simple random walk model. Normal diffusion is then treated (i) through formalizing the random walk model and deriving a classical diffusion equation, (ii) by using Fick’s law that leads again to the same diffusion equation, and (iii) by using a stochastic differential equation for the particle dynamics (the Langevin equation), which allows to determine the mean square displacement of particles. (iv) We discuss normal diffusion from the point of view of probability theory, applying the Central Limit Theorem to the random walk problem, and (v) we introduce the more general Fokker-Planck equation for diffusion that includes also advection. We turn then to anomalous diffusion, discussing first its formal characteristics, and proceeding to Continuous Time Random Walk (CTRW) as a model for anomalous diffusion. arXiv:0805.0419v1 [nlin.CD] 5 May 2008 It is shown how CTRW can be treated formally, the importance of probability distributions of the Levy type is explained, and we discuss the relation of CTRW to fractional diffusion equations and show how the latter can be derived from the CTRW equations.
    [Show full text]
  • Membrane Diffusion Occurs by a Continuous-Time Random Walk Sustained by Vesicular Trafficking
    bioRxiv preprint doi: https://doi.org/10.1101/208967; this version posted April 17, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. Membrane Diffusion Occurs by a Continuous-Time Random Walk Sustained by Vesicular Trafficking. Maria Goiko1,2, John R. de Bruyn2, Bryan Heit1,3*. Abstract Diffusion in cellular membranes is regulated by processes which occur over a range of spatial and temporal scales. These processes include membrane fluidity, inter-protein and inter-lipid interactions, interactions with membrane microdomains, interactions with the underlying cytoskeleton, and cellular processes which result in net membrane movement. The complex, non-Brownian diffusion that results from these processes has been difficult to characterize, and moreover, the impact of factors such as membrane recycling on membrane diffusion remains largely unexplored. We have used a careful statistical analysis of single-particle tracking data of the single-pass plasma membrane protein CD93 to show that the diffusion of this protein is well-described by a continuous-time random walk in parallel with an aging process mediated by membrane corrals. The overall result is an evolution in the diffusion of CD93: proteins initially diffuse freely on the cell surface, but over time, become increasingly trapped within diffusion-limiting membrane corrals. Stable populations of freely diffusing and corralled CD93 are maintained by an endocytic/exocytic process in which corralled CD93 is selectively endocytosed, while freely diffusing CD93 is replenished by exocytosis of newly synthesized and recycled CD93.
    [Show full text]
  • Fluorescence Correlation Spectroscopy 1
    Petra Schwille and Elke Haustein Fluorescence Correlation Spectroscopy 1 Fluorescence Correlation Spectroscopy An Introduction to its Concepts and Applications Petra Schwille and Elke Haustein Experimental Biophysics Group Max-Planck-Institute for Biophysical Chemistry Am Fassberg 11 D-37077 Göttingen Germany 2 Fluorescence Correlation Spectroscopy Petra Schwille and Elke Haustein Table of Contents TABLE OF CONTENTS 1 1. INTRODUCTION 3 2. EXPERIMENTAL REALIZATION 5 2.1. ONE-PHOTON EXCITATION 5 2.2. TWO-PHOTON EXCITATION 7 2.3. FLUORESCENT DYES 9 3. THEORETICAL CONCEPTS 10 3.1. AUTOCORRELATION ANALYSIS 10 3.2. CROSS-CORRELATION ANALYSIS 18 4. FCS APPLICATIONS 21 4.1. CONCENTRATION AND AGGREGATION MEASUREMENTS 21 4.2. CONSIDERATION OF RESIDENCE TIMES: DETERMINING MOBILITY AND MOLECULAR INTERACTIONS 23 4.2.1 DIFFUSION ANALYSIS 23 4.2.2 CONFINED AND ANOMALOUS DIFFUSION 24 4.2.3 ACTIVE TRANSPORT PHENOMENA IN TUBULAR STRUCTURES 24 4.2.4 DETERMINATION OF MOLECULAR INTERACTIONS 26 4.2.5 CONFORMATIONAL CHANGES 27 4.3. CONSIDERATION OF CROSS-CORRELATION AMPLITUDES: A DIRECT WAY TO MONITOR ASSOCIATION/DISSOCIATION AND ENZYME KINETICS 28 4.4. CONSIDERATION OF FAST FLICKERING: INTRAMOLECULAR DYNAMICS AND PROBING OF THE MICROENVIRONMENT 30 5. CONCLUSIONS AND OUTLOOK 31 6. REFERENCES 32 Petra Schwille and Elke Haustein Fluorescence Correlation Spectroscopy 3 1. Introduction Currently, it is almost impossible to open your daily newspaper without stumbling over words like gene manipulation, genetic engineering, cloning, etc. that reflect the tremendous impact of life sciences to our modern world. Press coverage of these features has long left behind the stage of merely reporting scientific facts. Instead, it focuses on general pros and cons, and expresses worries about what scientists have to do and what to refrain from.
    [Show full text]
  • Abdus Salam United Nations Educational, Scientific XA0101218 and Cultural Organization International Centre International Atomic Energy Agency for Theoretical Physics
    the nun abdus salam united nations educational, scientific XA0101218 and cultural organization international centre international atomic energy agency for theoretical physics FRACTAL DIFFUSION EQUATIONS: MICROSCOPIC MODELS WITH ANOMALOUS DIFFUSION AND ITS GENERALIZATIONS V.E. Arkhincheev 32/ 26 Available at: http://www.ictp.trieste.it/~pub_ off IC/2000/180 United Nations Educational Scientific and Cultural Organization and International Atomic Energy Agency THE ABDUS SALAM INTERNATIONAL CENTRE FOR THEORETICAL PHYSICS FRACTAL DIFFUSION EQUATIONS: MICROSCOPIC MODELS WITH ANOMALOUS DIFFUSION AND ITS GENERALIZATIONS V.E. Arkhincheev1 Buryat Science Center, Ulan-Ude, Russian Federation and The Abdus Salam International Centre for Theoretical Physics, Trieste, Italy. Abstract To describe the "anomalous" diffusion the generalized diffusion equations of fractal order are deduced from microscopic models with anomalous diffusion as Comb model and Levy flights. It is shown that two types of equations are possible: with fractional temporal and fractional spatial derivatives. The solutions of these equations are obtained and the physical sense of these fractional equaitions is discussed. The relation between diffusion and conductivity is studied and the well-known Einstein relation is generalized for the anomalous diffusion case. It is shown that for Levy flight diffusion the Ohm's law is not applied and the current depends on electric field in a nonlinear way due to the anomalous character of Levy flights. The results of numerical simulations, which confirmed this conclusion, are also presented. MIRAMARE - TRIESTE April 2001 'E-mail: [email protected] 1 Introduction. Classical diffusion, in which diffusing particle hops only to nearest sites, has been thoroughly studied, and many methods, related to the research of this phenomenon, have been developed.
    [Show full text]
  • Bacterial Hopping and Trapping in Porous Media Tapomoy Bhattacharjee1 and Sujit S
    Bacterial hopping and trapping in porous media Tapomoy Bhattacharjee1 and Sujit S. Datta2* 1 The Andlinger Center for Energy and the Environment, Princeton University, 86 Olden Street, Princeton, NJ 08544, USA 2 Department of Chemical and Biological Engineering, Princeton University, 41 Olden Street, Princeton, NJ 08544 USA Diverse processes—e.g. bioremediation, biofertilization, and microbial drug delivery—rely on bacterial migration in disordered, three-dimensional (3D) porous media. However, how pore- scale confinement alters bacterial motility is unknown due to the opacity of typical 3D media. As a result, models of migration are limited and often employ ad hoc assumptions. Here we reveal that the paradigm of run-and-tumble motility is dramatically altered in a porous medium. By directly visualizing individual E. coli, we find that the cells are intermittently and transiently trapped as they navigate the pore space, exhibiting diffusive behavior at long time scales. The trapping durations and the lengths of “hops” between traps are broadly distributed, reminiscent of transport in diverse other disordered systems; nevertheless, we show that these quantities can together predict the long-time bacterial translational diffusivity. Our work thus provides a revised picture of bacterial motility in complex media and yields principles for predicting cellular migration. * To whom correspondence should be addressed: [email protected]. 1 Introduction While bacterial motility is well-studied in unconfined liquid media and at flat surfaces,
    [Show full text]